Query 041890
Match_columns 375
No_of_seqs 165 out of 1025
Neff 7.7
Searched_HMMs 46136
Date Fri Mar 29 11:45:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041890.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041890hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03097 FHY3 Protein FAR-RED 100.0 3.3E-42 7.2E-47 362.9 25.9 295 21-349 156-496 (846)
2 PF00872 Transposase_mut: Tran 99.9 2E-24 4.3E-29 213.8 2.7 199 154-352 137-379 (381)
3 COG3328 Transposase and inacti 99.8 4.9E-18 1.1E-22 166.0 11.7 193 172-365 143-369 (379)
4 PF10551 MULE: MULE transposas 99.5 1.3E-14 2.9E-19 115.0 3.7 67 181-248 1-93 (93)
5 PF03108 DBD_Tnp_Mut: MuDR fam 99.0 7.5E-10 1.6E-14 82.5 5.4 43 1-43 25-67 (67)
6 PF03101 FAR1: FAR1 DNA-bindin 97.6 0.00024 5.2E-09 55.7 7.3 53 2-55 9-90 (91)
7 PF08731 AFT: Transcription fa 97.5 0.00051 1.1E-08 55.4 7.3 53 2-54 17-111 (111)
8 PF03106 WRKY: WRKY DNA -bindi 94.8 0.076 1.6E-06 38.4 5.2 41 13-53 19-59 (60)
9 PF06782 UPF0236: Uncharacteri 90.8 0.61 1.3E-05 47.9 6.8 105 216-326 263-377 (470)
10 smart00774 WRKY DNA binding do 90.3 0.44 9.6E-06 34.3 3.7 40 13-52 19-59 (59)
11 PF03050 DDE_Tnp_IS66: Transpo 87.5 0.29 6.4E-06 46.1 1.6 33 216-253 124-156 (271)
12 PF01610 DDE_Tnp_ISL3: Transpo 85.5 0.75 1.6E-05 42.6 3.2 37 216-252 61-97 (249)
13 PF04500 FLYWCH: FLYWCH zinc f 85.0 1.9 4.2E-05 30.4 4.5 46 3-52 14-62 (62)
14 PF13610 DDE_Tnp_IS240: DDE do 84.9 1.5 3.3E-05 37.1 4.6 57 175-234 2-81 (140)
15 PF13565 HTH_32: Homeodomain-l 79.3 4.2 9.1E-05 30.2 4.7 40 63-102 32-76 (77)
16 TIGR02867 spore_II_P stage II 66.7 22 0.00047 32.1 6.8 74 116-215 61-134 (196)
17 PF07454 SpoIIP: Stage II spor 51.0 28 0.0006 33.1 4.9 75 116-215 138-212 (268)
18 PF04937 DUF659: Protein of un 44.1 1.4E+02 0.0031 25.6 8.0 38 216-253 98-138 (153)
19 KOG3347 Predicted nucleotide k 40.3 76 0.0016 27.7 5.4 64 75-145 13-85 (176)
20 PF01498 HTH_Tnp_Tc3_2: Transp 35.0 31 0.00067 25.2 2.1 33 70-103 4-39 (72)
21 PF13592 HTH_33: Winged helix- 32.3 49 0.0011 23.5 2.7 21 77-97 2-22 (60)
22 KOG0489 Transcription factor z 31.3 12 0.00026 35.3 -0.8 36 320-355 180-215 (261)
23 TIGR03147 cyt_nit_nrfF cytochr 28.2 51 0.0011 27.6 2.5 36 62-97 54-93 (126)
24 PRK10144 formate-dependent nit 27.6 52 0.0011 27.5 2.4 36 62-97 54-93 (126)
25 PF08766 DEK_C: DEK C terminal 25.4 92 0.002 21.6 3.0 34 64-97 3-38 (54)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=3.3e-42 Score=362.85 Aligned_cols=295 Identities=13% Similarity=0.139 Sum_probs=241.2
Q ss_pred eecCCCceEEEEEEecCCCeEEEEEeCCCcccCCCCcccccchhhHHHHHhhhhhcCCCCCHHHHHHHHHHHhC----CC
Q 041890 21 CSDLMCDWKVSAAKVRKSNVFVLKEITPNHTCKRRNYKFPLRTKWNAEKFLHLWVQNPNIDFHILRYEIETCSG----FK 96 (375)
Q Consensus 21 C~~~~C~w~v~a~~~~~~~~~~I~~~~~~HtC~~~~~~~~~ss~~ia~~~~~~l~~~~~~~~~~i~~~l~~~~g----vs 96 (375)
|+.+||+++|.+.+ ...|+|.|+.++.+|||++..... ++ ...+.+...+....+ +.
T Consensus 156 ~tRtGC~A~m~Vk~-~~~gkW~V~~fv~eHNH~L~p~~~-~~-----------------~~~r~~~~~~~~~~~~~~~v~ 216 (846)
T PLN03097 156 CAKTDCKASMHVKR-RPDGKWVIHSFVKEHNHELLPAQA-VS-----------------EQTRKMYAAMARQFAEYKNVV 216 (846)
T ss_pred ccCCCCceEEEEEE-cCCCeEEEEEEecCCCCCCCCccc-cc-----------------hhhhhhHHHHHhhhhcccccc
Confidence 55678999999977 456899999999999998864331 11 011112222222111 21
Q ss_pred h-h------hhHHHHHHHHhHHHhhCChHHHHHHHHHHHHHHhhcCCCcEEEEEeeecCCCCcceeeEEEeehHHhHHHH
Q 041890 97 Y-P------TWKLEAIDKTAKLWLRTDHNYGYERLFQYKNEMLKVNSNNIVIIQTKTFDDPDVAVFDKMFILFADYSHAF 169 (375)
Q Consensus 97 ~-~------~~rak~~a~~~~~~~~g~~~~~y~~L~~yl~~l~~~Npgs~~~v~~~~~~~~~~~~f~r~f~~~~~~~~~f 169 (375)
. + .-+.++ +. .-.| +.+.|.+||.+++..||+++|.+++| +++ +++++||+++.++..|
T Consensus 217 ~~~~d~~~~~~~~r~--~~---~~~g----D~~~ll~yf~~~q~~nP~Ffy~~qlD---e~~--~l~niFWaD~~sr~~Y 282 (846)
T PLN03097 217 GLKNDSKSSFDKGRN--LG---LEAG----DTKILLDFFTQMQNMNSNFFYAVDLG---EDQ--RLKNLFWVDAKSRHDY 282 (846)
T ss_pred ccchhhcchhhHHHh--hh---cccc----hHHHHHHHHHHHHhhCCCceEEEEEc---cCC--CeeeEEeccHHHHHHH
Confidence 1 0 011111 11 2223 48899999999999999999999999 899 9999999999999999
Q ss_pred HhcCceEEEEeeeEEecCCCceEEEEEEEcCCCcEEhHHH--------------Hhhhhh----------hcCCCccHHH
Q 041890 170 KTTCRRLVIVDGWEIDSPYKSVMLVAVFRDANNVVLPIVF--------------CEGICI----------MCDGDNRVDE 225 (375)
Q Consensus 170 ~~~~r~vi~lD~t~lk~~~~g~ll~a~G~d~n~~~~~laf--------------l~~L~~----------isD~~~gl~~ 225 (375)
. ++++||.+|+||.+++|+++|.+++|+|+++|..++|+ |+.+.. |||++.+|.+
T Consensus 283 ~-~FGDvV~fDTTY~tN~y~~Pfa~FvGvNhH~qtvlfGcaLl~dEt~eSf~WLf~tfl~aM~gk~P~tIiTDqd~am~~ 361 (846)
T PLN03097 283 G-NFSDVVSFDTTYVRNKYKMPLALFVGVNQHYQFMLLGCALISDESAATYSWLMQTWLRAMGGQAPKVIITDQDKAMKS 361 (846)
T ss_pred H-hcCCEEEEeceeeccccCcEEEEEEEecCCCCeEEEEEEEcccCchhhHHHHHHHHHHHhCCCCCceEEecCCHHHHH
Confidence 8 89999999999999999999999999999999777765 344322 9999999999
Q ss_pred HHhhhcCCCcchhhhHHHHHHHhhhCCC-----hHhHHHHHHhhh-hccHHHHHHHHHH-HHhhchhhhchhhcc--ccc
Q 041890 226 AVSKSLPYAQYRQCCFSLYNKLKEQFPL-----APVYLLFWAACK-STNKVTFQQHMML-LQDQNRDCYGWLINR--EYH 296 (375)
Q Consensus 226 Ai~~vfP~a~h~~C~~Hl~~N~~~~~~~-----~~l~~~~~~~~~-a~t~~ef~~~~~~-i~~~~~~a~~~L~~~--~~~ 296 (375)
||.+|||++.|++|+|||.+|+.+++.. +.+...|..+.+ +.+++||+..|.+ |.+++....+||... .++
T Consensus 362 AI~~VfP~t~Hr~C~wHI~~~~~e~L~~~~~~~~~f~~~f~~cv~~s~t~eEFE~~W~~mi~ky~L~~n~WL~~LY~~Re 441 (846)
T PLN03097 362 VISEVFPNAHHCFFLWHILGKVSENLGQVIKQHENFMAKFEKCIYRSWTEEEFGKRWWKILDRFELKEDEWMQSLYEDRK 441 (846)
T ss_pred HHHHHCCCceehhhHHHHHHHHHHHhhHHhhhhhHHHHHHHHHHhCCCCHHHHHHHHHHHHHhhcccccHHHHHHHHhHh
Confidence 9999999999999999999999999863 588999999886 7899999999988 467788999999984 899
Q ss_pred ccccccCCCCcccceecCchHHHHhHHHhhc--cCCchhhHHHHHHHHHHHhhhh
Q 041890 297 CWALYCMPEWAKGTDITISAAEQLRSWLLKY--LDMNVANRFTTITRETAKNFEK 349 (375)
Q Consensus 297 ~W~~~~f~~~r~~~~~TtN~~Es~N~~l~~~--r~~pi~~~~e~i~~~~~~~~~~ 349 (375)
+|+++||++.++++|.||+.+||+|+.|+++ +..++..|++.+.+.+-.++.+
T Consensus 442 kWapaY~k~~F~agm~sTqRSES~Ns~fk~yv~~~tsL~~Fv~qye~~l~~~~ek 496 (846)
T PLN03097 442 QWVPTYMRDAFLAGMSTVQRSESINAFFDKYVHKKTTVQEFVKQYETILQDRYEE 496 (846)
T ss_pred hhhHHHhcccccCCcccccccccHHHHHHHHhCcCCCHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999994 7899999999998888776654
No 2
>PF00872 Transposase_mut: Transposase, Mutator family; InterPro: IPR001207 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. The mutator family of transposases consists of a number of elements that include, mutator from maize, IsT2 from Thiobacillus ferrooxidans, Is256 from Staphylococcus aureus, Is1201 from Lactobacillus helveticus, Is1081 from Mycobacterium bovis, IsRm3 from Rhizobium meliloti and others. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=99.89 E-value=2e-24 Score=213.83 Aligned_cols=199 Identities=14% Similarity=0.115 Sum_probs=163.4
Q ss_pred eeeEEEeehHHhHHHHHh----cC-ceEEEEeeeEEecCCCce-----EEEEEEEcCCCcEEhHHH--------------
Q 041890 154 VFDKMFILFADYSHAFKT----TC-RRLVIVDGWEIDSPYKSV-----MLVAVFRDANNVVLPIVF-------------- 209 (375)
Q Consensus 154 ~f~r~f~~~~~~~~~f~~----~~-r~vi~lD~t~lk~~~~g~-----ll~a~G~d~n~~~~~laf-------------- 209 (375)
.+.|+.-.+.+.+..|++ .. .|+|+|||+|++.+.+|. +++|+|+|.+|+..+||+
T Consensus 137 ~vSri~~~~~~~~~~w~~R~L~~~~y~~l~iD~~~~kvr~~~~~~~~~~~v~iGi~~dG~r~vLg~~~~~~Es~~~W~~~ 216 (381)
T PF00872_consen 137 TVSRITKQLDEEVEAWRNRPLESEPYPYLWIDGTYFKVREDGRVVKKAVYVAIGIDEDGRREVLGFWVGDRESAASWREF 216 (381)
T ss_pred hhhhhhhhhhhhHHHHhhhccccccccceeeeeeecccccccccccchhhhhhhhhcccccceeeeecccCCccCEeeec
Confidence 556666666677777865 34 678999999999986654 699999999999999997
Q ss_pred Hhhhhh---------hcCCCccHHHHHhhhcCCCcchhhhHHHHHHHhhhCCCh---HhHHHHHHhhhhccHHHHHHHHH
Q 041890 210 CEGICI---------MCDGDNRVDEAVSKSLPYAQYRQCCFSLYNKLKEQFPLA---PVYLLFWAACKSTNKVTFQQHMM 277 (375)
Q Consensus 210 l~~L~~---------isD~~~gl~~Ai~~vfP~a~h~~C~~Hl~~N~~~~~~~~---~l~~~~~~~~~a~t~~ef~~~~~ 277 (375)
|++|+. |+|+++||.+||+++||++.||+|++|+++|+.++++.+ .+..+++.+..+.+.+++...++
T Consensus 217 l~~L~~RGl~~~~lvv~Dg~~gl~~ai~~~fp~a~~QrC~vH~~RNv~~~v~~k~~~~v~~~Lk~I~~a~~~e~a~~~l~ 296 (381)
T PF00872_consen 217 LQDLKERGLKDILLVVSDGHKGLKEAIREVFPGAKWQRCVVHLMRNVLRKVPKKDRKEVKADLKAIYQAPDKEEAREALE 296 (381)
T ss_pred chhhhhccccccceeeccccccccccccccccchhhhhheechhhhhccccccccchhhhhhccccccccccchhhhhhh
Confidence 566655 999999999999999999999999999999999999853 77888888888888888777776
Q ss_pred HH----HhhchhhhchhhcccccccccccCCCCcccceecCchHHHHhHHHhhc----cCCchhhHHHHHHHHHHHhhhh
Q 041890 278 LL----QDQNRDCYGWLINREYHCWALYCMPEWAKGTDITISAAEQLRSWLLKY----LDMNVANRFTTITRETAKNFEK 349 (375)
Q Consensus 278 ~i----~~~~~~a~~~L~~~~~~~W~~~~f~~~r~~~~~TtN~~Es~N~~l~~~----r~~pi~~~~e~i~~~~~~~~~~ 349 (375)
++ ...+|++.++|.+...+.|+..-||...+..++|||.+||+|+.||+. +.+|-.+.+..+-..++...++
T Consensus 297 ~f~~~~~~kyp~~~~~l~~~~~~~~tf~~fP~~~~~~i~TTN~iEsln~~irrr~~~~~~Fp~~~s~lr~~~~~~~e~~~ 376 (381)
T PF00872_consen 297 EFAEKWEKKYPKAAKSLEENWDELLTFLDFPPEHRRSIRTTNAIESLNKEIRRRTKVVGIFPNEESALRLVYAVLMEANK 376 (381)
T ss_pred hcccccccccchhhhhhhhccccccceeeecchhccccchhhhccccccchhhhccccccCCCHHHHHHHHHHHHHHHHh
Confidence 64 556899999999988889998888877665589999999999999984 3366666666666666666666
Q ss_pred hcc
Q 041890 350 KVL 352 (375)
Q Consensus 350 r~~ 352 (375)
+|.
T Consensus 377 ~w~ 379 (381)
T PF00872_consen 377 KWR 379 (381)
T ss_pred hhc
Confidence 654
No 3
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=99.75 E-value=4.9e-18 Score=166.03 Aligned_cols=193 Identities=13% Similarity=0.055 Sum_probs=146.8
Q ss_pred cCceEEEEeeeEEecC--CCceEEEEEEEcCCCcEEhHHH-------------Hhhhhh---------hcCCCccHHHHH
Q 041890 172 TCRRLVIVDGWEIDSP--YKSVMLVAVFRDANNVVLPIVF-------------CEGICI---------MCDGDNRVDEAV 227 (375)
Q Consensus 172 ~~r~vi~lD~t~lk~~--~~g~ll~a~G~d~n~~~~~laf-------------l~~L~~---------isD~~~gl~~Ai 227 (375)
+.+|++++||+|+|.| -+..+++|+|++.+|+..+|++ |.+|+. ++|+++||.+||
T Consensus 143 ~~~~~v~~D~~~~k~r~v~~~~~~ia~Gv~~eG~reilg~~~~~~e~~~w~~~l~~l~~rgl~~v~l~v~Dg~~gl~~aI 222 (379)
T COG3328 143 GDYPYVYLDAKYVKVRSVRNKAVYIAIGVTEEGRREILGIWVGVRESKFWLSFLLDLKNRGLSDVLLVVVDGLKGLPEAI 222 (379)
T ss_pred cCceEEEEecceeehhhhhhheeeeeeccCcccchhhhceeeecccchhHHHHHHHHHhccccceeEEecchhhhhHHHH
Confidence 4678999999999999 3556899999999999999997 344444 899999999999
Q ss_pred hhhcCCCcchhhhHHHHHHHhhhCCCh---HhHHHHHHhhhhccHHHHHHHHH----HHHhhchhhhchhhccccccccc
Q 041890 228 SKSLPYAQYRQCCFSLYNKLKEQFPLA---PVYLLFWAACKSTNKVTFQQHMM----LLQDQNRDCYGWLINREYHCWAL 300 (375)
Q Consensus 228 ~~vfP~a~h~~C~~Hl~~N~~~~~~~~---~l~~~~~~~~~a~t~~ef~~~~~----~i~~~~~~a~~~L~~~~~~~W~~ 300 (375)
.++||.+.||+|..|+.+|+..+.+.+ .+...+..+..+.+.++....++ .+....|....|+.+...+.|..
T Consensus 223 ~~v~p~a~~Q~C~vH~~Rnll~~v~~k~~d~i~~~~~~I~~a~~~e~~~~~~~~~~~~w~~~yP~i~~~~~~~~~~~~~F 302 (379)
T COG3328 223 SAVFPQAAVQRCIVHLVRNLLDKVPRKDQDAVLSDLRSIYIAPDAEEALLALLAFSELWGKRYPAILKSWRNALEELLPF 302 (379)
T ss_pred HHhccHhhhhhhhhHHHhhhhhhhhhhhhHHHHhhhhhhhccCCcHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHhccc
Confidence 999999999999999999999999864 55667777777776666544444 45667889999999888888887
Q ss_pred ccCCCC-cccceecCchHHHHhHHHhhc-cCCchhhHHHHHHHHHHHhhhhh-cccccccCccccccC
Q 041890 301 YCMPEW-AKGTDITISAAEQLRSWLLKY-LDMNVANRFTTITRETAKNFEKK-VLGWVGLGAGQHHSS 365 (375)
Q Consensus 301 ~~f~~~-r~~~~~TtN~~Es~N~~l~~~-r~~pi~~~~e~i~~~~~~~~~~r-~~~~~~~~~~~~~~~ 365 (375)
.-||.. |.. ++|||.+|++|+.++.. +-.++++--+.+.+.+....++- +.+...+||+.+++.
T Consensus 303 ~~fp~~~r~~-i~ttN~IE~~n~~ir~~~~~~~~fpn~~sv~k~~y~~~~~~~~~~r~~~~~~~a~~~ 369 (379)
T COG3328 303 FAFPSEIRKI-IYTTNAIESLNKLIRRRTKVVGIFPNEESVEKLVYLVLNEANKWTRSLRGWRLAMSR 369 (379)
T ss_pred ccCcHHHHhH-hhcchHHHHHHHHHHHHHhhhccCCCHHHHHHHHHHHHHHhhhccccccchhhhhHH
Confidence 777765 445 99999999999988863 44444444444444443333331 344556788777654
No 4
>PF10551 MULE: MULE transposase domain; InterPro: IPR018289 This entry represents a domain found in Mutator-like elements (MULE)-encoded tranposases, some of which also contain a zinc-finger motif [, ]. This domain is also found in a transposase for the insertion sequence element IS256 in transposon Tn4001 [].
Probab=99.49 E-value=1.3e-14 Score=114.97 Aligned_cols=67 Identities=27% Similarity=0.389 Sum_probs=60.4
Q ss_pred eeEEecCCCceEEE---EEEEcCCCcEEhHHH--------------Hhhhhh---------hcCCCccHHHHHhhhcCCC
Q 041890 181 GWEIDSPYKSVMLV---AVFRDANNVVLPIVF--------------CEGICI---------MCDGDNRVDEAVSKSLPYA 234 (375)
Q Consensus 181 ~t~lk~~~~g~ll~---a~G~d~n~~~~~laf--------------l~~L~~---------isD~~~gl~~Ai~~vfP~a 234 (375)
|||.+++| |+++. ++|.|++|+.+|+|| |+.|+. +||++.|+.+||+++||++
T Consensus 1 ~T~~tn~~-~~l~~~~~~~~~d~~~~~~~v~~~l~~~e~~~~~~~~l~~~~~~~~~~p~~ii~D~~~~~~~Ai~~vfP~~ 79 (93)
T PF10551_consen 1 GTYKTNKY-GPLLYLMIAVGIDGNGRGFPVAFALVSSESEESYEWFLEKLKEAMPQKPKVIISDFDKALINAIKEVFPDA 79 (93)
T ss_pred Cccccccc-cccceeceEEEEcCCCCEEEEEEEEEcCCChhhhHHHHHHhhhccccCceeeeccccHHHHHHHHHHCCCc
Confidence 79999999 98875 999999999999998 444433 8999999999999999999
Q ss_pred cchhhhHHHHHHHh
Q 041890 235 QYRQCCFSLYNKLK 248 (375)
Q Consensus 235 ~h~~C~~Hl~~N~~ 248 (375)
.|++|.||+.+|++
T Consensus 80 ~~~~C~~H~~~n~k 93 (93)
T PF10551_consen 80 RHQLCLFHILRNIK 93 (93)
T ss_pred eEehhHHHHHHhhC
Confidence 99999999999974
No 5
>PF03108 DBD_Tnp_Mut: MuDR family transposase; InterPro: IPR004332 The plant MuDR transposase domain is present in plant proteins that are presumed to be the transposases for Mutator transposable elements [, ]. The function of these proteins is unknown. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=98.98 E-value=7.5e-10 Score=82.45 Aligned_cols=43 Identities=26% Similarity=0.643 Sum_probs=41.1
Q ss_pred CCccEEEEEEeecCeEEEEEeecCCCceEEEEEEecCCCeEEE
Q 041890 1 MRDGIKLYVMENTSTFINCECSDLMCDWKVSAAKVRKSNVFVL 43 (375)
Q Consensus 1 ~~~~~~~~~~rs~~~r~~~~C~~~~C~w~v~a~~~~~~~~~~I 43 (375)
|+++|+|++.+||++|++++|.+.+|||+|+|++.++++.|+|
T Consensus 25 i~~~~~~~v~ksd~~r~~~~C~~~~C~Wrv~as~~~~~~~~~I 67 (67)
T PF03108_consen 25 IKNGFEFKVKKSDKKRYRAKCKDKGCPWRVRASKRKRSDTFQI 67 (67)
T ss_pred HhcCcEEEEeccCCEEEEEEEcCCCCCEEEEEEEcCCCCEEEC
Confidence 5789999999999999999999999999999999999999987
No 6
>PF03101 FAR1: FAR1 DNA-binding domain; InterPro: IPR004330 Phytochrome A is the primary photoreceptor for mediating various far-red light-induced responses in higher plants. It has been found that the proteins governing this response, which include FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and FAR-RED-IMPAIRED RESPONSE1 (FAR1), are a pair of homologous proteins sharing significant sequence homology to mutator-like transposases. These proteins appear to be novel transcription factors, which are essential for activating the expression of FHY1 and FHL (for FHY1-like) and related genes, whose products are required for light-induced phytochrome A nuclear accumulation and subsequent light responses in plants. The FRS (FAR1 Related Sequences) family of proteins share a similar domain structure to mutator-like transposases, including an N-terminal C2H2 zinc finger domain, a central putative core transposase domain, and a C-terminal SWIM motif (named after SWI2/SNF and MuDR transposases). It seems plausible that the FRS family represent transcription factors derived from mutator-like transposases [, ]. This entry represents a domain found in FAR1 and FRS proteins. It contains a WRKY like fold and is therefore most likely a zinc binding DNA-binding domain.
Probab=97.61 E-value=0.00024 Score=55.71 Aligned_cols=53 Identities=11% Similarity=0.249 Sum_probs=44.4
Q ss_pred CccEEEEEEeecCe-------EEEEEeec----------------------CCCceEEEEEEecCCCeEEEEEeCCCccc
Q 041890 2 RDGIKLYVMENTST-------FINCECSD----------------------LMCDWKVSAAKVRKSNVFVLKEITPNHTC 52 (375)
Q Consensus 2 ~~~~~~~~~rs~~~-------r~~~~C~~----------------------~~C~w~v~a~~~~~~~~~~I~~~~~~HtC 52 (375)
..||.++..++.+. ++.++|.. ++||++|.+.+.+ .+.|.|+.+..+|||
T Consensus 9 ~~GF~vr~~~s~~~~~~~~~~~~~~~C~r~G~~~~~~~~~~~~~r~~~s~ktgC~a~i~v~~~~-~~~w~v~~~~~~HNH 87 (91)
T PF03101_consen 9 RHGFSVRKSSSRKSKKNGEIKRVTFVCSRGGKYKSKKKNEEKRRRNRPSKKTGCKARINVKRRK-DGKWRVTSFVLEHNH 87 (91)
T ss_pred cCCeEEEEeeeEeCCCCceEEEEEEEECCcccccccccccccccccccccccCCCEEEEEEEcc-CCEEEEEECcCCcCC
Confidence 45788887776555 78888865 6999999999888 899999999999999
Q ss_pred CCC
Q 041890 53 KRR 55 (375)
Q Consensus 53 ~~~ 55 (375)
+..
T Consensus 88 ~L~ 90 (91)
T PF03101_consen 88 PLC 90 (91)
T ss_pred CCC
Confidence 864
No 7
>PF08731 AFT: Transcription factor AFT; InterPro: IPR014842 AFT (activator of iron transcription) is an iron regulated transcriptional activator that regulates the expression of genes involved in iron homeostasis. This entry includes the paralogous pair of transcription factors AFT1 and AFT2.
Probab=97.46 E-value=0.00051 Score=55.42 Aligned_cols=53 Identities=17% Similarity=0.365 Sum_probs=48.0
Q ss_pred CccEEEEEEeecCeEEEEEeec------------------------------------------CCCceEEEEEEecCCC
Q 041890 2 RDGIKLYVMENTSTFINCECSD------------------------------------------LMCDWKVSAAKVRKSN 39 (375)
Q Consensus 2 ~~~~~~~~~rs~~~r~~~~C~~------------------------------------------~~C~w~v~a~~~~~~~ 39 (375)
.+|+++.+-|||+..+.++|.. ..|||+|+|+......
T Consensus 17 ~~Gi~iVIerSd~~ki~FkCk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~k~t~srk~~CPFriRA~yS~k~k 96 (111)
T PF08731_consen 17 PQGIGIVIERSDKKKIVFKCKNGKRYRHKKKKKGQAQAQQKESTSGNKNKSSKKKKKKRTKSRKNTCPFRIRANYSKKNK 96 (111)
T ss_pred hcCceEEEEecCCceEEEEEecCCCcccccccccccccccccccccccccccccccCCcccccccCCCeEEEEEEEecCC
Confidence 3689999999999999999964 2699999999999999
Q ss_pred eEEEEEeCCCcccCC
Q 041890 40 VFVLKEITPNHTCKR 54 (375)
Q Consensus 40 ~~~I~~~~~~HtC~~ 54 (375)
.|.|+.+++.|+|+.
T Consensus 97 ~W~lvvvnn~HnH~l 111 (111)
T PF08731_consen 97 KWTLVVVNNEHNHPL 111 (111)
T ss_pred eEEEEEecCCcCCCC
Confidence 999999999999974
No 8
>PF03106 WRKY: WRKY DNA -binding domain; InterPro: IPR003657 The WRKY domain is a 60 amino acid region that is defined by the conserved amino acid sequence WRKYGQK at its N-terminal end, together with a novel zinc-finger- like motif. The WRKY domain is found in one or two copies in a superfamily of plant transcription factors involved in the regulation of various physiological programs that are unique to plants, including pathogen defence, senescence, trichome development and the biosynthesis of secondary metabolites. The WRKY domain binds specifically to the DNA sequence motif (T)(T)TGAC(C/T), which is known as the W box. The invariant TGAC core of the W box is essential for function and WRKY binding []. Some proteins known to contain a WRKY domain include Arabidopsis thaliana ZAP1 (Zinc-dependent Activator Protein-1) and AtWRKY44/TTG2, a protein involved in trichome development and anthocyanin pigmentation; and wild oat ABF1-2, two proteins involved in the gibberelic acid-induced expression of the alpha-Amy2 gene. Structural studies indicate that this domain is a four-stranded beta-sheet with a zinc binding pocket, forming a novel zinc and DNA binding structure []. The WRKYGQK residues correspond to the most N-terminal beta-strand, which enables extensive hydrophobic interactions, contributing to the structural stability of the beta-sheet.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2AYD_A 1WJ2_A 2LEX_A.
Probab=94.85 E-value=0.076 Score=38.45 Aligned_cols=41 Identities=12% Similarity=0.130 Sum_probs=33.5
Q ss_pred cCeEEEEEeecCCCceEEEEEEecCCCeEEEEEeCCCcccC
Q 041890 13 TSTFINCECSDLMCDWKVSAAKVRKSNVFVLKEITPNHTCK 53 (375)
Q Consensus 13 ~~~r~~~~C~~~~C~w~v~a~~~~~~~~~~I~~~~~~HtC~ 53 (375)
.--|-..+|+..+|+.+-.+.+..+++...++++.++|||+
T Consensus 19 ~~pRsYYrCt~~~C~akK~Vqr~~~d~~~~~vtY~G~H~h~ 59 (60)
T PF03106_consen 19 PYPRSYYRCTHPGCPAKKQVQRSADDPNIVIVTYEGEHNHP 59 (60)
T ss_dssp TCEEEEEEEECTTEEEEEEEEEETTCCCEEEEEEES--SS-
T ss_pred ceeeEeeeccccChhheeeEEEecCCCCEEEEEEeeeeCCC
Confidence 34577799999999999999998877888889999999996
No 9
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=90.80 E-value=0.61 Score=47.90 Aligned_cols=105 Identities=20% Similarity=0.179 Sum_probs=72.4
Q ss_pred hcCCCccHHHHHhhhcCCCcchhhhHHHHHHHhhhCCC-hHhHHHHHHhhhhccHHHHHHHHHHHHhhc--h-------h
Q 041890 216 MCDGDNRVDEAVSKSLPYAQYRQCCFSLYNKLKEQFPL-APVYLLFWAACKSTNKVTFQQHMMLLQDQN--R-------D 285 (375)
Q Consensus 216 isD~~~gl~~Ai~~vfP~a~h~~C~~Hl~~N~~~~~~~-~~l~~~~~~~~~a~t~~ef~~~~~~i~~~~--~-------~ 285 (375)
.+||.++|.+++. .+|++.|++..+|+.+.+.+.++. +.+...++++.......++...++.+...- + +
T Consensus 263 ngDGa~WIk~~~~-~~~~~~~~LD~FHl~k~i~~~~~~~~~~~~~~~~al~~~d~~~l~~~L~~~~~~~~~~~~~~~i~~ 341 (470)
T PF06782_consen 263 NGDGASWIKEGAE-FFPKAEYFLDRFHLNKKIKQALSHDPELKEKIRKALKKGDKKKLETVLDTAESCAKDEEERKKIRK 341 (470)
T ss_pred eCCCcHHHHHHHH-hhcCceEEecHHHHHHHHHHHhhhChHHHHHHHHHHHhcCHHHHHHHHHHHHHhhhchHHHHHHHH
Confidence 8999999988776 999999999999999999998874 577787888888778888888887765432 1 2
Q ss_pred hhchhhcccccccccccCCCCcccceecCchHHHHhHHHhh
Q 041890 286 CYGWLINREYHCWALYCMPEWAKGTDITISAAEQLRSWLLK 326 (375)
Q Consensus 286 a~~~L~~~~~~~W~~~~f~~~r~~~~~TtN~~Es~N~~l~~ 326 (375)
...||.+ +|...-....+.+ +......|+.+..+..
T Consensus 342 ~~~Yl~~----n~~~i~~y~~~~~-~~g~g~ee~~~~~~s~ 377 (470)
T PF06782_consen 342 LRKYLLN----NWDGIKPYREREG-LRGIGAEESVSHVLSY 377 (470)
T ss_pred HHHHHHH----CHHHhhhhhhccC-CCccchhhhhhhHHHH
Confidence 3444443 4432100000112 4555667777766543
No 10
>smart00774 WRKY DNA binding domain. The WRKY domain is a DNA binding domain found in one or two copies in a superfamily of plant transcription factors. These transcription factors are involved in the regulation of various physiological programs that are unique to plants, including pathogen defense, senescence and trichome development. The domain is a 60 amino acid region that is defined by the conserved amino acid sequence WRKYGQK at its N-terminal end, together with a novel zinc-finger-like motif. It binds specifically to the DNA sequence motif (T)(T)TGAC(C/T), which is known as the W box. The invariant TGAC core is essential for function and WRKY binding.
Probab=90.29 E-value=0.44 Score=34.30 Aligned_cols=40 Identities=15% Similarity=0.085 Sum_probs=32.3
Q ss_pred cCeEEEEEeec-CCCceEEEEEEecCCCeEEEEEeCCCccc
Q 041890 13 TSTFINCECSD-LMCDWKVSAAKVRKSNVFVLKEITPNHTC 52 (375)
Q Consensus 13 ~~~r~~~~C~~-~~C~w~v~a~~~~~~~~~~I~~~~~~HtC 52 (375)
..-|-..+|+. .+|+.+-.+.+...++...++++.++|||
T Consensus 19 ~~pRsYYrCt~~~~C~a~K~Vq~~~~d~~~~~vtY~g~H~h 59 (59)
T smart00774 19 PFPRSYYRCTYSQGCPAKKQVQRSDDDPSVVEVTYEGEHTH 59 (59)
T ss_pred cCcceEEeccccCCCCCcccEEEECCCCCEEEEEEeeEeCC
Confidence 33466789998 89999888887766666777899999998
No 11
>PF03050 DDE_Tnp_IS66: Transposase IS66 family ; InterPro: IPR004291 Transposase proteins are necessary for efficient DNA transposition. This family includes the bacterial insertion sequence (IS) element, IS66, from Agrobacterium tumefaciens []. IS66 may cause genetic and structural variations of the T region and the vir region of the octopine Ti plasmids []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=87.48 E-value=0.29 Score=46.14 Aligned_cols=33 Identities=15% Similarity=0.225 Sum_probs=27.2
Q ss_pred hcCCCccHHHHHhhhcCCCcchhhhHHHHHHHhhhCCC
Q 041890 216 MCDGDNRVDEAVSKSLPYAQYRQCCFSLYNKLKEQFPL 253 (375)
Q Consensus 216 isD~~~gl~~Ai~~vfP~a~h~~C~~Hl~~N~~~~~~~ 253 (375)
+||+.+|-.. +..+.|+.|+.|+.|.+.+....
T Consensus 124 vsD~y~~Y~~-----~~~~~hq~C~AH~~R~~~~~~~~ 156 (271)
T PF03050_consen 124 VSDGYSAYNK-----LAGITHQLCWAHLRRDFQDAAES 156 (271)
T ss_pred eccccccccc-----ccccccccccccccccccccccc
Confidence 8999888654 33789999999999999877653
No 12
>PF01610 DDE_Tnp_ISL3: Transposase; InterPro: IPR002560 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. This family includes the IS204 [], IS1001 [], IS1096 [] and IS1165 [] transposases. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=85.50 E-value=0.75 Score=42.61 Aligned_cols=37 Identities=16% Similarity=0.122 Sum_probs=34.6
Q ss_pred hcCCCccHHHHHhhhcCCCcchhhhHHHHHHHhhhCC
Q 041890 216 MCDGDNRVDEAVSKSLPYAQYRQCCFSLYNKLKEQFP 252 (375)
Q Consensus 216 isD~~~gl~~Ai~~vfP~a~h~~C~~Hl~~N~~~~~~ 252 (375)
++|...+..+||++.||+|.+-.-.+|+++++.+.+.
T Consensus 61 ~~Dm~~~y~~~~~~~~P~A~iv~DrFHvvk~~~~al~ 97 (249)
T PF01610_consen 61 SMDMSPPYRSAIREYFPNAQIVADRFHVVKLANRALD 97 (249)
T ss_pred EcCCCccccccccccccccccccccchhhhhhhhcch
Confidence 9999999999999999999999999999999987554
No 13
>PF04500 FLYWCH: FLYWCH zinc finger domain; InterPro: IPR007588 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a potential FLYWCH Zn-finger domain found in a number of eukaryotic proteins. FLYWCH is a C2H2-type zinc finger characterised by five conserved hydrophobic residues, containing the conserved sequence motif: F/Y-X(n)-L-X(n)-F/Y-X(n)-WXCX(6-12)CX(17-22)HXH where X indicates any amino acid. This domain was first characterised in Drosophila Modifier of mdg4 proteins, Mod(mgd4), putative chromatin modulators involved in higher order chromatin domains. Mod(mdg4) proteins share a common N-terminal BTB/POZ domain, but differ in their C-terminal region, most containing C-terminal FLYWCH zinc finger motifs []. The FLYWCH domain in Mod(mdg4) proteins has a putative role in protein-protein interactions; for example, Mod(mdg4)-67.2 interacts with DNA-binding protein Su(Hw) via its FLYWCH domain. FLYWCH domains have been described in other proteins as well, including suppressor of killer of prune, Su(Kpn), which contains 4 terminal FLYWCH zinc finger motifs in a tandem array and a C-terminal glutathione SH-transferase (GST) domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2RPR_A.
Probab=85.01 E-value=1.9 Score=30.36 Aligned_cols=46 Identities=15% Similarity=0.214 Sum_probs=25.5
Q ss_pred ccEEEEEEeecCeEEEEEeecC---CCceEEEEEEecCCCeEEEEEeCCCccc
Q 041890 3 DGIKLYVMENTSTFINCECSDL---MCDWKVSAAKVRKSNVFVLKEITPNHTC 52 (375)
Q Consensus 3 ~~~~~~~~rs~~~r~~~~C~~~---~C~w~v~a~~~~~~~~~~I~~~~~~HtC 52 (375)
+++.|...+.......-.|... +|+.+|... .+. ..|.....+|||
T Consensus 14 ~Gy~y~~~~~~~~~~~WrC~~~~~~~C~a~~~~~--~~~--~~~~~~~~~HnH 62 (62)
T PF04500_consen 14 DGYRYYFNKRNDGKTYWRCSRRRSHGCRARLITD--AGD--GRVVRTNGEHNH 62 (62)
T ss_dssp TTEEEEEEEE-SS-EEEEEGGGTTS----EEEEE----T--TEEEE-S---SS
T ss_pred CCeEEECcCCCCCcEEEEeCCCCCCCCeEEEEEE--CCC--CEEEECCCccCC
Confidence 5778888888889999999884 899999987 222 344455578886
No 14
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=84.86 E-value=1.5 Score=37.09 Aligned_cols=57 Identities=18% Similarity=-0.043 Sum_probs=43.0
Q ss_pred eEEEEeeeEEecCCCceEEEEEEEcCCCcEEhHHH--------------Hhhhhh---------hcCCCccHHHHHhhhc
Q 041890 175 RLVIVDGWEIDSPYKSVMLVAVFRDANNVVLPIVF--------------CEGICI---------MCDGDNRVDEAVSKSL 231 (375)
Q Consensus 175 ~vi~lD~t~lk~~~~g~ll~a~G~d~n~~~~~laf--------------l~~L~~---------isD~~~gl~~Ai~~vf 231 (375)
+.+.+|-||++.+-+ ..++--++|.+++ +|+| |+.+.. ++|+.+....|+.++.
T Consensus 2 ~~w~~DEt~iki~G~-~~yl~~aiD~~~~--~l~~~ls~~Rd~~aA~~Fl~~~l~~~~~~p~~ivtDk~~aY~~A~~~l~ 78 (140)
T PF13610_consen 2 DSWHVDETYIKIKGK-WHYLWRAIDAEGN--ILDFYLSKRRDTAAAKRFLKRALKRHRGEPRVIVTDKLPAYPAAIKELN 78 (140)
T ss_pred CEEEEeeEEEEECCE-EEEEEEeeccccc--chhhhhhhhcccccceeeccccceeeccccceeecccCCccchhhhhcc
Confidence 568899999987644 3455667888888 5666 222211 9999999999999999
Q ss_pred CCC
Q 041890 232 PYA 234 (375)
Q Consensus 232 P~a 234 (375)
|..
T Consensus 79 ~~~ 81 (140)
T PF13610_consen 79 PEG 81 (140)
T ss_pred ccc
Confidence 874
No 15
>PF13565 HTH_32: Homeodomain-like domain
Probab=79.35 E-value=4.2 Score=30.22 Aligned_cols=40 Identities=13% Similarity=0.168 Sum_probs=32.4
Q ss_pred hhhHHHHHhhhhhcCCCCCHHHHHHHHHHHhC--C--Ch-hhhHH
Q 041890 63 TKWNAEKFLHLWVQNPNIDFHILRYEIETCSG--F--KY-PTWKL 102 (375)
Q Consensus 63 s~~ia~~~~~~l~~~~~~~~~~i~~~l~~~~g--v--s~-~~~ra 102 (375)
...+.+.+.+.+..+|.+++.+|.+.|.+++| + |. ++||.
T Consensus 32 ~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~ 76 (77)
T PF13565_consen 32 DPEQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRI 76 (77)
T ss_pred cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHh
Confidence 34455667788888999999999999999999 4 77 77763
No 16
>TIGR02867 spore_II_P stage II sporulation protein P. Stage II sporulation protein P is a protein of the endospore formation program in a number of lineages in the Firmicutes (low-GC Gram-positive bacteria). It is expressed in the mother cell compartment, under control of Sigma-E. SpoIIP, along with SpoIIM and SpoIID, is one of three major proteins involved in engulfment of the forespore by the mother cell. This protein family is named for the single member in Bacillus subtilis, although most sporulating bacteria have two members.
Probab=66.69 E-value=22 Score=32.14 Aligned_cols=74 Identities=11% Similarity=0.096 Sum_probs=50.7
Q ss_pred ChHHHHHHHHHHHHHHhhcCCCcEEEEEeeecCCCCcceeeEEEeehHHhHHHHHhcCceEEEEeeeEEecCCCceEEEE
Q 041890 116 DHNYGYERLFQYKNEMLKVNSNNIVIIQTKTFDDPDVAVFDKMFILFADYSHAFKTTCRRLVIVDGWEIDSPYKSVMLVA 195 (375)
Q Consensus 116 ~~~~~y~~L~~yl~~l~~~Npgs~~~v~~~~~~~~~~~~f~r~f~~~~~~~~~f~~~~r~vi~lD~t~lk~~~~g~ll~a 195 (375)
++..+|.......+++.+.||+..+.+++..|..+. -...+-+ .|+.-.+++.+
T Consensus 61 ~y~~sY~~Sr~tv~~~l~~~p~i~~viDiHRDs~~~---------------------~~~t~~i-----nG~~~Aki~fV 114 (196)
T TIGR02867 61 NYEQSYDRSRETVKKALKENKDLKYIIDLHRDSVRR---------------------KKTTVNI-----NGESVAKVMFV 114 (196)
T ss_pred cHHHHHHHHHHHHHHHHHHCCCceEEEEeecCCCCC---------------------CcceEEE-----CCEEEEEEEEE
Confidence 668899999999999999999988888887432222 0122222 33334468899
Q ss_pred EEEcCCCcEEhHHHHhhhhh
Q 041890 196 VFRDANNVVLPIVFCEGICI 215 (375)
Q Consensus 196 ~G~d~n~~~~~lafl~~L~~ 215 (375)
+|.+.-+...-++|-+.|..
T Consensus 115 vG~~np~~~~N~~fA~~l~~ 134 (196)
T TIGR02867 115 IGKNNPHFEKNLQLANKLHA 134 (196)
T ss_pred EcCCCCCHHHHHHHHHHHHH
Confidence 99887666666777555544
No 17
>PF07454 SpoIIP: Stage II sporulation protein P (SpoIIP); InterPro: IPR010897 This family contains the bacterial stage II sporulation protein P (SpoIIP) (approximately 350 residues long). It has been shown that a block in polar cytokinesis in Bacillus subtilis is mediated partly by transcription of spoIID, spoIIM and spoIIP. This inhibition of polar division is involved in the locking in of asymmetry after the formation of a polar septum during sporulation []. SpoIIP is one of the three genes (spoIID, spoIIM and spoIIP, [, , ]), under the control of sigma E, that have been shown to be essential for the engulfment of the forespore by the mother cell. Their products are involved in degradation of the septal peptidoglycan and mutations in spoIID, spoIIM or spoIIP block sporulation at morphological stage II, prior to the stage of engulfment. These three genes are absolutely conserved (sometimes even duplicated) in all endospore formers [].
Probab=50.98 E-value=28 Score=33.06 Aligned_cols=75 Identities=21% Similarity=0.215 Sum_probs=52.7
Q ss_pred ChHHHHHHHHHHHHHHhhcCCCcEEEEEeeecCCCCcceeeEEEeehHHhHHHHHhcCceEEEEeeeEEecCCCceEEEE
Q 041890 116 DHNYGYERLFQYKNEMLKVNSNNIVIIQTKTFDDPDVAVFDKMFILFADYSHAFKTTCRRLVIVDGWEIDSPYKSVMLVA 195 (375)
Q Consensus 116 ~~~~~y~~L~~yl~~l~~~Npgs~~~v~~~~~~~~~~~~f~r~f~~~~~~~~~f~~~~r~vi~lD~t~lk~~~~g~ll~a 195 (375)
++..||.+-...++++.+.||+..+.+++..|...+ .-.. ++-+.|+.-.+++++
T Consensus 138 ~y~~sY~~Sr~tv~~~l~~~p~i~~~iDiHRDs~~~--------------------~~~~-----t~~InG~~~Aki~fV 192 (268)
T PF07454_consen 138 SYNQSYKRSRETVKKALKENPDIKVVIDIHRDSVPD--------------------REKT-----TTTINGKNYAKIMFV 192 (268)
T ss_pred hhHHHHHHHHHHHHHHHHHCCCceEEEEecCCCCCc--------------------cccc-----eEEECCEEeeEEEEE
Confidence 778899999999999999999999999888533221 0011 223344555679999
Q ss_pred EEEcCCCcEEhHHHHhhhhh
Q 041890 196 VFRDANNVVLPIVFCEGICI 215 (375)
Q Consensus 196 ~G~d~n~~~~~lafl~~L~~ 215 (375)
+|.+.-+...-++|-+.|..
T Consensus 193 vG~~np~~~~N~~fA~~l~~ 212 (268)
T PF07454_consen 193 VGRDNPNWEKNLAFAKQLHA 212 (268)
T ss_pred EcCCCCCHHHHHHHHHHHHH
Confidence 99997676666777544443
No 18
>PF04937 DUF659: Protein of unknown function (DUF 659); InterPro: IPR007021 These are transposase-like proteins with no known function.
Probab=44.13 E-value=1.4e+02 Score=25.59 Aligned_cols=38 Identities=16% Similarity=0.235 Sum_probs=30.6
Q ss_pred hcCCCccHHHHH---hhhcCCCcchhhhHHHHHHHhhhCCC
Q 041890 216 MCDGDNRVDEAV---SKSLPYAQYRQCCFSLYNKLKEQFPL 253 (375)
Q Consensus 216 isD~~~gl~~Ai---~~vfP~a~h~~C~~Hl~~N~~~~~~~ 253 (375)
|||......+|- .+-+|.-.+--|..|-+.-+.+.+..
T Consensus 98 VTDn~~~~~~a~~~L~~k~p~ifw~~CaaH~inLmledi~k 138 (153)
T PF04937_consen 98 VTDNASNMKKAGKLLMEKYPHIFWTPCAAHCINLMLEDIGK 138 (153)
T ss_pred hccCchhHHHHHHHHHhcCCCEEEechHHHHHHHHHHHHhc
Confidence 899988887774 44489999999999998888877654
No 19
>KOG3347 consensus Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]
Probab=40.27 E-value=76 Score=27.68 Aligned_cols=64 Identities=14% Similarity=0.173 Sum_probs=46.8
Q ss_pred hcCCCCCHHHHHHHHHHHhCCCh-hhhH-HHHHHHHhHHHhhCChHHHHH-------HHHHHHHHHhhcCCCcEEEEEee
Q 041890 75 VQNPNIDFHILRYEIETCSGFKY-PTWK-LEAIDKTAKLWLRTDHNYGYE-------RLFQYKNEMLKVNSNNIVIIQTK 145 (375)
Q Consensus 75 ~~~~~~~~~~i~~~l~~~~gvs~-~~~r-ak~~a~~~~~~~~g~~~~~y~-------~L~~yl~~l~~~Npgs~~~v~~~ 145 (375)
...|+.....+.+.|.+..|+.| .+.+ +|+. .+++.+++.|. ++.++|+.+... -|.+++....
T Consensus 13 tGTPG~GKstl~~~lae~~~~~~i~isd~vkEn------~l~~gyDE~y~c~i~DEdkv~D~Le~~m~~-Gg~IVDyHgC 85 (176)
T KOG3347|consen 13 TGTPGTGKSTLAERLAEKTGLEYIEISDLVKEN------NLYEGYDEEYKCHILDEDKVLDELEPLMIE-GGNIVDYHGC 85 (176)
T ss_pred eCCCCCCchhHHHHHHHHhCCceEehhhHHhhh------cchhcccccccCccccHHHHHHHHHHHHhc-CCcEEeeccc
Confidence 35788888899999999999777 5544 4554 66777777775 888998877777 4666665543
No 20
>PF01498 HTH_Tnp_Tc3_2: Transposase; InterPro: IPR002492 Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of Caenorhabditis elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in []. Tc3 is a member of the Tc1/mariner family of transposable elements. This entry also includes histone-lysine N-methyltransferase SETMAR, which is a SET domain and mariner transposase fusion gene-containing protein. This histone methyltransferase has sequence-specific DNA-binding activity and recognises the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element. This protein has DNA nicking activity, and has in vivo end joining activity and may mediate genomic integration of foreign DNA [, , , ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated, 0015074 DNA integration; PDB: 3K9K_B 3F2K_B 3K9J_B 1U78_A.
Probab=34.98 E-value=31 Score=25.20 Aligned_cols=33 Identities=15% Similarity=0.246 Sum_probs=12.9
Q ss_pred HhhhhhcCCCCCHHHHHHHHHHHhC--CCh-hhhHHH
Q 041890 70 FLHLWVQNPNIDFHILRYEIETCSG--FKY-PTWKLE 103 (375)
Q Consensus 70 ~~~~l~~~~~~~~~~i~~~l~~~~g--vs~-~~~rak 103 (375)
+...++.+|..+..+|...+.+. | ||. ++++.-
T Consensus 4 I~~~v~~~p~~s~~~i~~~l~~~-~~~vS~~TI~r~L 39 (72)
T PF01498_consen 4 IVRMVRRNPRISAREIAQELQEA-GISVSKSTIRRRL 39 (72)
T ss_dssp ------------HHHHHHHT----T--S-HHHHHHHH
T ss_pred HHHHHHHCCCCCHHHHHHHHHHc-cCCcCHHHHHHHH
Confidence 44566778889999999888887 7 777 666643
No 21
>PF13592 HTH_33: Winged helix-turn helix
Probab=32.35 E-value=49 Score=23.47 Aligned_cols=21 Identities=24% Similarity=0.222 Sum_probs=16.5
Q ss_pred CCCCCHHHHHHHHHHHhCCCh
Q 041890 77 NPNIDFHILRYEIETCSGFKY 97 (375)
Q Consensus 77 ~~~~~~~~i~~~l~~~~gvs~ 97 (375)
+..++.++|.+.|.+.|||+|
T Consensus 2 ~~~wt~~~i~~~I~~~fgv~y 22 (60)
T PF13592_consen 2 GGRWTLKEIAAYIEEEFGVKY 22 (60)
T ss_pred CCcccHHHHHHHHHHHHCCEE
Confidence 345778889999999999666
No 22
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=31.32 E-value=12 Score=35.30 Aligned_cols=36 Identities=14% Similarity=0.386 Sum_probs=32.6
Q ss_pred HhHHHhhccCCchhhHHHHHHHHHHHhhhhhccccc
Q 041890 320 LRSWLLKYLDMNVANRFTTITRETAKNFEKKVLGWV 355 (375)
Q Consensus 320 ~N~~l~~~r~~pi~~~~e~i~~~~~~~~~~r~~~~~ 355 (375)
+|+.|-+.|..-|...|...++.|--||.+|++-|+
T Consensus 180 fN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~K 215 (261)
T KOG0489|consen 180 FNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWK 215 (261)
T ss_pred cccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHH
Confidence 577888889999999999999999999999988885
No 23
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=28.21 E-value=51 Score=27.58 Aligned_cols=36 Identities=14% Similarity=-0.046 Sum_probs=29.3
Q ss_pred chhhHHHHHhhhhhc--CCCCCHHHHHHHHHHHhC--CCh
Q 041890 62 RTKWNAEKFLHLWVQ--NPNIDFHILRYEIETCSG--FKY 97 (375)
Q Consensus 62 ss~~ia~~~~~~l~~--~~~~~~~~i~~~l~~~~g--vs~ 97 (375)
|..-+|.-++..++. ..+.+-.+|.+.+.++|| |-|
T Consensus 54 S~a~iA~dmR~~Vr~~i~~G~Sd~eI~~~~v~RYG~~Vly 93 (126)
T TIGR03147 54 SNSPIAYDLRHEVYSMVNEGKSNQQIIDFMTARFGDFVLY 93 (126)
T ss_pred cCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhcCCeEEe
Confidence 445678877777775 578899999999999999 666
No 24
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=27.59 E-value=52 Score=27.50 Aligned_cols=36 Identities=11% Similarity=-0.085 Sum_probs=29.5
Q ss_pred chhhHHHHHhhhhhc--CCCCCHHHHHHHHHHHhC--CCh
Q 041890 62 RTKWNAEKFLHLWVQ--NPNIDFHILRYEIETCSG--FKY 97 (375)
Q Consensus 62 ss~~ia~~~~~~l~~--~~~~~~~~i~~~l~~~~g--vs~ 97 (375)
|..-+|.-++..++. ..+.+..+|.+.+.+.|| |-|
T Consensus 54 Sna~iA~dmR~~Vr~~i~~G~sd~eI~~~~v~RYG~~Vl~ 93 (126)
T PRK10144 54 SNAPVAVSMRHQVYSMVAEGKSEVEIIGWMTERYGDFVRY 93 (126)
T ss_pred cCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhcCCeEEe
Confidence 455778877777775 678899999999999999 666
No 25
>PF08766 DEK_C: DEK C terminal domain; InterPro: IPR014876 DEK is a chromatin associated protein that is linked with cancers and autoimmune disease. This domain is found at the C-terminal of DEK and is of clinical importance since it can reverse the characteristic abnormal DNA-mutagen sensitivity in fibroblasts from ataxia-telangiectasia (A-T) patients []. The structure of this domain shows it to be homologous to the E2F/DP transcription factor family []. This domain is also found in chitin synthase proteins like Q8TF96 from SWISSPROT, and in protein phosphatases such as Q6NN85 from SWISSPROT. ; PDB: 1Q1V_A.
Probab=25.35 E-value=92 Score=21.59 Aligned_cols=34 Identities=12% Similarity=0.122 Sum_probs=22.6
Q ss_pred hhHHHHHhhhhhc-C-CCCCHHHHHHHHHHHhCCCh
Q 041890 64 KWNAEKFLHLWVQ-N-PNIDFHILRYEIETCSGFKY 97 (375)
Q Consensus 64 ~~ia~~~~~~l~~-~-~~~~~~~i~~~l~~~~gvs~ 97 (375)
..|...+.++++. + .+++.+++.+.|.+.||++.
T Consensus 3 ~~i~~~i~~iL~~~dl~~vT~k~vr~~Le~~~~~dL 38 (54)
T PF08766_consen 3 EEIREAIREILREADLDTVTKKQVREQLEERFGVDL 38 (54)
T ss_dssp HHHHHHHHHHHTTS-GGG--HHHHHHHHHHH-SS--
T ss_pred HHHHHHHHHHHHhCCHhHhhHHHHHHHHHHHHCCCc
Confidence 4566677777775 3 67899999999999999665
Done!